SMTL ID : 5y5y.1

V/A-type ATPase/synthase from Thermus thermophilus, peripheral domain, rotational state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-2-2-1-mer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: G.231, S.232, G.233, K.234, T.235, V.236, E.261, F.419, N.498, A.499, Y.500 Chain F: R.360 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain F Hydrogen bonds: A:P.229, A:G.231, A:S.232, A:G.233, A:K.234, A:T.235, A:E.261, A:N.498, A:N.498, A:A.499 Salt bridges: A:K.234, F:R.360, F:R.360 pi-Stacking: A:F.419, A:Y.500 ADP.2: 12 residues within 4Å: Chain C: F.230, G.231, S.232, G.233, K.234, T.235, V.236, R.417, H.418, F.419 Chain E: L.358, R.360 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:G.231, C:S.232, C:G.233, C:T.235, C:T.235, C:V.236, C:H.418, C:H.418, C:F.419 Salt bridges: C:K.234, E:R.360, E:R.360 pi-Stacking: C:F.419, C:F.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakanishi, A. et al., Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus. Nat Commun (2018)

Release Date

2018-01-24

Peptides

V-type ATP synthase alpha chain: ABC
V-type ATP synthase beta chain: DEF
V-type ATP synthase subunit D: G
V-type ATP synthase subunit F: H
V-type ATP synthase, subunit (VAPC-THERM): IK
V-type ATP synthase subunit E: JL
V-type ATP synthase subunit C: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

K
K

J
J

L
L

M
M

V-type ATP synthase alpha chain

V-type ATP synthase beta chain

V-type ATP synthase subunit D

V-type ATP synthase subunit F

V-type ATP synthase, subunit (VAPC-THERM)

V-type ATP synthase subunit E

V-type ATP synthase subunit C

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